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A Cambridge computer programmer who backed a US Army private accused of leaking classified information has settled with the federal government in a case that began when federal agents seized the programmer’s laptop as he was returning from a Mexican vacation.

David House, a former MIT researcher who cofounded an organization to raise money for Bradley Manning, accused the Department of Homeland Security of violating his civil rights when he passed through a Chicago airport in November 2010.

Homeland Security agents did not have a warrant when they seized House’s ­laptop, camera, and a flash drive, then asked him questions about his ­relationship with Manning, according to House’s lawsuit. Manning is accused of leaking classified information about the wars in Afghanistan and Iraq that was posted on WikiLeaks and published by The New York Times and other news organizations.

More than two years after the encounter, the government has agreed to destroy any data it retrieved from the laptop and the other devices. The government also agreed to hand over copies of reports of the investigation into House. In return, House agreed to drop his lawsuit.

The case “dramatically ­illustrates the dangers of the government’s claim to extra­ordinary powers to search at the border,” said John ­Reinstein, an attorney for the America Civil Liberties Union, which filed the lawsuit on House’s behalf. “That ­authority is not without its limit.”

House could not be reached for comment Thursday. A spokeswoman for the US Department of Justice ­declined to comment.

In his lawsuit, House said that after he helped create the Bradley Manning Support Network in June 2010, he was placed on a government watchlist and questioned repeat­edly at his Cambridge home by investigators from the Defense and State departments and the FBI.

On Nov. 3, 2010, House ­arrived at O’Hare International Airport in Chicago. He was rushing to make his connection to Boston when he was stopped by two federal agents, who told him he would not be making that flight, according to the lawsuit.

The agents asked him about Manning, whether he had any connections to WikiLeaks, and about his work for the Bradley Manning Support Network, which says it has raised $1.1 million for Manning’s ­defense. The laptop the agents seized from House had information about donors, including their names.

The Department of Justice had tried to have the lawsuit thrown out, asserting that the government has the authority to conduct routine searches at a US border.

The government also ­argued that federal officials are not prohibited by the Constitution from searching electronic ­devices because they are connected to a specific group or ­organization.

But US District Court Judge Denise J. Casper rejected the ­arguments.

“That the initial search and seizure occurred at the border does not strip House of his First Amendment rights, ­particularly given the allegations in the complaint that he was targeted specifically ­because of his ­association with the Support Network,” she wrote in her March 2012 decision.

Manning’s trial is scheduled to begin June 3. Military prosecutors must prove that ­Manning believed that the files he released could be used to harm the United States or aid a foreign enemy.

Manning has already pleaded guilty to 10 charges related to the leaks, but prosecutors are trying for a conviction on more serious charges, including multiple counts of violating the ­Espionage Act, which outlaws releasing information related to the military.

Elizabeth Goitein, codirector of the Liberty and National Security Program at the Brennan Center for Justice, called the Espionage Act a ­
Draconian law that prosecutors in this case are abusing.

“The Espionage Act should be used only for spies, traitors, and enemies of the state,” she said. “I think it’s ­inappropriate to use it for whistle-blowers or Bradley Manning, who did not act with ill intent.”

Many have hailed Manning as a hero who sought to ­expose wrongdoing by the ­Army while others have ­labeled him a traitor. Goitein said she believes Manning, who released 750,000 files of wide-ranging information from diplomatic cables to videos of civilians being killed, is neither.

“To me there is a recklessness here that does suggest some culpability,” she said.